crossing96/oncoscreening huggingface dataset:
Label-free detection of bladder cancer and kidney cancer plasma based on SERS and multivariate statistical algorithm.	In this study, we mainly aimed to investigate the diagnostic potential of surface-enhanced Raman spectroscopy for bladder cancer and kidney cancer which are the most common cancers of the urinary system, and evaluate the classification ability of three statistical algorithms: principal component analysis-linear discriminate analysis (PCA-LDA), partial least square-random forest (PLS-RF), and partial least square-support vector machine (PLS-SVM). The plasma of 26 bladder cancer patients, 38 kidney cancer patients and 39 normal subjects was mixed with the same volume of silver nanoparticles, respectively, and then high-quality SERS signal was obtained. The SERS spectra in the range of 400-1800 cm(-1) were compared and analyzed. There were some significant differences in SERS peak intensity, which may reflect the changes in the content of some biomacromolecules in the plasma of cancer patients. Based on the three algorithms of PCA-LDA, PLS-RF and PLS-SVM, the classification accuracy of SERS spectra of plasma from cancer patients and normal subjects was 98.1%, 100% and 100%, respectively. In addition, the classification accuracy of the three diagnostic algorithms to classify the SERS spectra of bladder cancer and kidney cancer was 81.3%, 91.7%, and 98.4%, respectively. This exploratory work demonstrates that SERS combined with PLS-SVM algorithm has superior performance for clinical screening of bladder cancer and kidney cancer through peripheral plasma.	bladder
A new approach to generating virtual samples to enhance classification accuracy with small data-a case of bladder cancer.	In the medical field, researchers are often unable to obtain the sufficient samples in a short period of time necessary to build a stable data-driven forecasting model used to classify a new disease. To address the problem of small data learning, many studies have demonstrated that generating virtual samples intended to augment the amount of training data is an effective approach, as it helps to improve forecasting models with small datasets. One of the most popular methods used in these studies is the mega-trend-diffusion (MTD) technique, which is widely used in various fields. The effectiveness of the MTD technique depends on the degree of data diffusion. However, data diffusion is seriously affected by extreme values. In addition, the MTD method only considers data fitted using a unimodal triangular membership function. However, in fact, data may come from multiple distributions in the real world. Therefore, considering the fact that data comes from multi-distributions, in this paper, a distance-based mega-trend-diffusion (DB-MTD) technique is proposed to appropriately estimate the degree of data diffusion with less impacts from extreme values. In the proposed method, it is assumed that the data is fitted by the triangular and trapezoidal membership functions to generate virtual samples. In addition, a possibility evaluation mechanism is proposed to measure the applicability of the virtual samples. In our experiment, two bladder cancer datasets are used to verify the effectiveness of the proposed DB-MTD method. The experimental results demonstrated that the proposed method outperforms other VSG techniques in classification and regression items for small bladder cancer datasets.	bladder
Real-world treatment patterns and clinical outcomes of Japanese patients with non-muscle invasive bladder cancer receiving intravesical bacillus Calmette-Guérin treatment.	OBJECTIVES: To investigate current patterns and outcomes of intravesical bacillus Calmette-Guérin treatment in Japanese patients with bladder cancer, including the proportion of patients completing induction therapy, and time to subsequent treatments. METHODS: This retrospective cohort study utilized administrative claims data from the Medical Data Vision Co., Ltd. database to identify patients with a diagnosis of bladder cancer who had received ≥1 prescription of intravesical bacillus Calmette-Guérin between April 2008 and September 2015, and had ≥1 database record dated ≥12 weeks after the initial bacillus Calmette-Guérin dose. Patients were followed until September 2018, the last date of available data, or in-hospital death. Patients receiving six doses of bacillus Calmette-Guérin at intervals of <21 days were considered to have completed induction according to guidelines. Time from initial bacillus Calmette-Guérin dose to subsequent bladder cancer treatment after the end of treatment was defined as the recurrence-free duration. RESULTS: Of 6140 patients identified (median age 73.0 years; 83.4% males), 4588 (74.7%) completed induction and 1552 (25.3%) did not. Median recurrence-free duration was 64.4, 77.7, and 31.6 months in the overall, complete-induction and incomplete-induction cohorts, respectively. Corresponding 3-year recurrence-free rate was 56.3%, 59.0%, and 48.2% in these groups. The rate of cystectomy was approximately 6% at 5 years in all cohorts. CONCLUSIONS: Approximately 75% of Japanese patients who undergo intravesical bacillus Calmette-Guérin treatment receive a guideline-compliant induction regimen, but outcomes were not satisfactory, highlighting the need for more effective treatments for non-muscle invasive bladder cancer.	bladder
MTHFD2 is a potential oncogene for its strong association with poor prognosis and high level of immune infiltrates in urothelial carcinomas of bladder.	"BACKGROUND: The bifunctional methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase (MTHFD2) has been reported to play an oncogenic role in various types of cancers. However, the function of MTHFD2 in urothelial carcinomas of bladder (UCB) and its association with tumor immune infiltration remains unknown. We aim to examine the suitability of MTHFD2 to be a novel biomarker of bladder cancer and whether MTHFD2 is linked to immune infiltration. METHODS: RNA sequencing data and clinical information (bladder cancer samples: normal samples = 414: 19) were downloaded from The Cancer Genome Atlas official website. Western blot analysis was performed to detect MTHFD2 expression in human bladder cancer (BLCA) cells and normal urothelial cell line SV-HUC-1. Associations between MTHFD2 expression and clinicopathological features were analyzed using Mann Whitney U test or Kruskal-Wallis H test. The ""survival"" and ""survminer"" packages were utilized to plot Kaplan-Meier survival curves. Moreover, the gene set enrichment analysis (GSEA) was conducted using a clusterProfiler package. The correlation of MTHFD2 expression with immune infiltration level was estimated using the single sample GSEA (ssGSEA) algorithm. Furthermore, associations between MTHFD2 and immune checkpoint genes were evaluated using the correlation analysis. RESULTS: Transcriptome analysis manifested that MTHFD2 was highly expressed in UCB tissues than normal bladder tissues, which was further confirmed by western blot analysis in human BLCA cells and SV-HUC-1 cells. Moreover, MTHFD2 high expression was significantly associated with the advanced disease progression. Also, the high expression of MTHFD2 was correlated with poor prognosis, and MTHFD2 was considered as an independent prognostic factor for disease specific survival. Furthermore, a number of cancer-related pathways were enriched in MTHFD2 high group, including NF-κB activation, JAK/STAT, and cancer immunotherapy by PD1 blockade. Several immune checkpoint molecules were also strongly associated with MTHFD2 expression, including PDCD1, CD274, CTLA4, CD276, LAG3, HAVCR2, and TIGIT. CONCLUSIONS: MTHFD2 expression was remarkably elevated in UCB, suggesting that MTHFD2 could be a promising biomarker for BLCA as well as novel target for anti-cancer immunotherapy since its close association with immune infiltration."	bladder
Two cases of Bacillus Calmette-Guérin cystitis treated with hyperbaric oxygen.	Hyperbaric oxygen (HBO2) therapy is a UHMS-approved treatment for radiation cystitis and has been used for other causes of cystitis such as cyclophosphamide-induced hemorrhagic cystitis and interstitial cystitis, among others. Immunotherapy with Bacillus Calmette-Guérin (BCG) is the most effective treatment of non-muscle invasive bladder cancer. BCG acts as a non-specific stimulant of the reticuloendothelial system, causing a local inflammatory response. BCG attaches to bladder tumor cells as well as urothelial cells which then stimulates an immune response involving a multitude of cytokines and local migration of polymorphonuclear cells that leads to death of the cancer cells. The typical protocol of a single six-week course has been shown to provide long-term protection from tumor recurrence and to reduce disease progression. Irritative bladder side effects are common, but serious side effects are uncommon. Two cases of severe BCG-cystitis treated with HBO2 are presented. Two male patients with bladder cancer were treated with intravesicular BCG. Each developed complications of pain, spasms, urinary frequency and nocturia; one developed gross hematuria. Cystoscopy showed friable mucosa. They failed standard medical therapy and were referred for HBO2. They were treated in a multiplace chamber at 2.2-2.4 ATA. One patient received 60 and the other 40 treatments. Both experienced substantial reduction in their symptoms. BCG cystitis may be considered for HBO2 if other standard therapy has failed.	bladder
Identification of distinct genomic features reveals frequent somatic AHNAK and PTEN mutations predominantly in primary malignant melanoma presenting in the ureter.	BACKGROUND: Primary malignant melanoma of the ureter is extremely rare. Genetic variants to the increased risk of developing the disease have not yet been investigated. METHODS: Tumour mutation profiling for primary malignant melanoma of the ureter was performed by whole-exome sequencing. Immunohistochemistry was performed to verify histopathological features and the variants of predisposing genes and driver mutation genes. Furthermore, we conducted a literature review and Surveillance, Epidemiology and End Result-based study by searching public databases. RESULTS: We identified 38 somatic single nucleotide variants and 9 somatic insertions and deletions (INDELs) in tumour specimens. After filtering with the Cancer Gene Census database, seven predisposing genes and two driver mutation genes were identified. Moreover, the immunohistochemical profile showed that tumour cells were positive for Melan-A, melanoma gp100 human melanoma black 45 (HMB45), S100 beta and P53. The expression levels of two driver mutation genes (phosphatase and tensin homolog (PTEN) and desmoyokin (AHNAK) and five predisposing genes (AT-rich interaction domain 1B (ARID1B), catalase, eukaryotic translation initiation factor 4 gamma 3 (EIF4G3), ANK3 and collagen type I) were significantly downregulated in tumour tissues compared to paracancerous tissues. In the literature review and Surveillance, Epidemiology and End Results-based study, patients with primary malignant melanoma of the urinary tract had worse clinical outcomes than patients with primary urothelial carcinoma after 1:2 propensity score matching (P = 0.010). Additionally, Cox multivariate analysis for patients with primary malignant melanoma of the urinary tract indicated that distant metastasis (hazard ratio = 1.185; P = 0.044) was an independent predictor for overall survival, and tumour focality (hazard ratio = 0.602; P = 0.017) and non-surgery (hazard ratio = 0.434; P = 0.003) were independent factors for tumour progression. CONCLUSIONS: Our study is the first to provide evidence that the distinct phenotypes of primary malignant melanoma of the ureter may be due to different genetic variations. The prognosis of primary malignant melanoma of the urinary tract was poorer than that of primary urothelial carcinoma of the urinary tract.	bladder
The Accuracy of Sequential Urethral Frozen Section and its Impact on Urethral Recurrence After Radical Cystectomy.	OBJECTIVE: To assess the accuracy of frozen section analysis (FSA) for detecting and eliminating malignant urethral margins during radical cystectomy (RC) for bladder cancer (BC) and its impact on urethral recurrence. METHODS: Urethral margins were initially examined by FSA in 217 patients at RC. When positive, additional resections were performed. Subsequently, all specimens were re-examined on formalin-fixed, paraffin-embedded sections (FFPE). Malignancy was defined as either the presence of carcinoma in situ, high-grade or invasive tumor cells at the urethral margin. Kaplan-Meier analysis was used to assess the impact of the final urethral margin status on urethral recurrence. Multinomial logistic regression addressed independent risk factors for a positive final urethral margin. RESULTS: At initial examination, urethral margins were positive on FSA and FFPE in 21 (9.7%) and 17 (7.8) patients, respectively. The corresponding sensitivity, specificity, positive and negative predictive values were 88.2%, 97.0%, 71.4% and 99.0% (overall accuracy: 96.3%). After initial FSA, 23 patients (including 2 with equivocal histological findings) received re-resections (median: 1, total range: 1-3). Persistent positive margins were detected on FSA in 10 (43.5%) while none of these margins were positive on FFPE (overall accuracy: 52.2%). A positive urethral FSA at initial assessment was the only independent risk for a positive final urethral margin. The 3-year urethral recurrence-free survival was 99.1% for patients with negative margins on initial assessment (I), 100% for those with negative final margins after re-resection (II) and 83.3% for patients with positive final margins (III; P= .013 for I/II vs. III). CONCLUSIONS: The accuracy of FSA for detecting malignant urethral margins is high on initial examination but drops considerably in case of re-resection while most positive margins at initial FSA are converted to negative final ones on FFPE. Conversion of a positive to a negative margin was associated with a lower risk of urethral recurrence.	bladder
Anti-CSF-1R emactuzumab in combination with anti-PD-L1 atezolizumab in advanced solid tumor patients naïve or experienced for immune checkpoint blockade.	BACKGROUND: This phase 1b study (NCT02323191) evaluated the safety, antitumor activity, pharmacokinetics, and pharmacodynamics of colony-stimulating factor-1 receptor-blocking monoclonal antibody (mAb) emactuzumab in combination with the programmed cell death-1 ligand (PD-L1)-blocking mAb atezolizumab in patients with advanced solid tumors naïve or experienced for immune checkpoint blockers (ICBs). METHODS: Emactuzumab (500-1350 mg flat) and atezolizumab (1200 mg flat) were administered intravenously every 3 weeks. Dose escalation of emactuzumab was conducted using the 3+3 design up to the maximum tolerated dose (MTD) or optimal biological dose (OBD). Extension cohorts to evaluate pharmacodynamics and clinical activity were conducted in metastatic ICB-naive urothelial bladder cancer (UBC) and ICB-pretreated melanoma (MEL), non-small cell lung cancer (NSCLC) and UBC patients. RESULTS: Overall, 221 patients were treated. No MTD was reached and the OBD was determined at 1000 mg of emactuzumab in combination with 1200 mg of atezolizumab. Grade ≥3 treatment-related adverse events occurred in 25 (11.3%) patients of which fatigue and rash were the most common (14 patients (6.3%) each). The confirmed objective response rate (ORR) was 9.8% for ICB-naïve UBC, 12.5% for ICB-experienced NSCLC, 8.3% for ICB-experienced UBC and 5.6% for ICB-experienced MEL patients, respectively. Tumor biopsy analyses demonstrated increased activated CD8 +tumor infiltrating T lymphocytes (TILs) associated with clinical benefit in ICB-naïve UBC patients and less tumor-associated macrophage (TAM) reduction in ICB-experienced compared with ICB-naïve patients. CONCLUSION: Emactuzumab in combination with atezolizumab demonstrated a manageable safety profile with increased fatigue and skin rash over usual atezolizumab monotherapy. A considerable ORR was particularly seen in ICB-experienced NSCLC patients. Increase ofCD8 +TILs under therapy appeared to be associated with persistence of a TAM subpopulation.	bladder
Phase 1/2 Trial Results of a Large Surface Area Microparticle Docetaxel for the Treatment of High-Risk Nonmuscle-Invasive Bladder Cancer.	PURPOSE: We investigated the safety, preliminary efficacy, and immune effects of large surface area microparticle docetaxel (LSAM-DTX) administered by direct injection after transurethral resection of bladder tumor (TURBT), and by intravesical instillation in high-risk nonmuscle-invasive bladder cancer. MATERIALS AND METHODS: The trial followed an open-label 3+3 dose escalation with additional enrollment at the high dose. After TURBT, subjects received direct injection LSAM-DTX into the resection site and intravesical LSAM-DTX, followed by 6-week induction and 3-week maintenance intravesical LSAM-DTX courses. Tumor recurrence was evaluated by cytology, cystoscopy, or biopsy. Pharmacokinetic analysis of blood and multiplex immunofluorescence of tumor microenvironment occurred pre- and post-LSAM-DTX. RESULTS: Nineteen subjects were enrolled, 14 with prior bacillus Calmette-Guérin exposure and 16 with ≥1 prior TURBT. Direct injection and intravesical LSAM-DTX were well tolerated. In the 3 lowest dose escalation cohorts the median recurrence-free survival was 5.4 months (10 patients, median followup 8.6 months). In the high-dose and expansion cohorts median recurrence-free survival was significantly increased (p <0.05, hazard ratio 0.29) to 12.2 months (9 patients, median followup 12.4 months). Systemic docetaxel exposure was negligible and increases in antitumor immune cells were found in the tumor microenvironment along with elevations in the PD-1, PD-L1 and CTLA-4 immune checkpoint inhibitor targets. CONCLUSIONS: Post-TURBT direct injection and intravesical LSAM-DTX were well tolerated and demonstrated clinical response for patients with high-risk nonmuscle-invasive bladder cancer. Favorable immune cell infiltration and checkpoint receptor increases following LSAM-DTX treatment warrants investigation alone as well as in combination with immune checkpoint inhibitor therapy.	bladder
Association between use of ERAS protocols and complications after radical cystectomy.	PURPOSE: Implementation of enhanced recovery protocols in cystectomy patients has significantly changed the perioperative course of this major operation. This paper summarizes evidence based interventions to enhance the postoperative course of radical cystectomy. METHODS: A comprehensive search of PubMed and Embase databases was performed and also the results of our institutional enhanced recovery protocol were discussed. RESULTS: One of the major advantages of such changes is the reduced rate of postoperative gastrointestinal (GI) complications especially postoperative ileus which could be contributed to several components of these protocols. However, Alvimopan is the only component which its use is supported by level I evidence. Although there are some evidence suggesting the decreased rate of urinary tract infection with the use of prophylactic antibiotics and wound complications by the use of negative wound pressure devices, their clear benefit is yet to be shown. Although robotic approach has proven advantages in intraoperative blood loss and postoperative blood transfusion rate, surgical team's experience and dedicated infrastructure seem to be more influential in optimized outcome than just the surgical approach. CONCLUSION: current evidence suggests that such protocols have not only reached the goal of maintaining complication rate while decreasing length of hospital stay, but it might have caused a decrease in the rate of low-grade complications, especially GI complications.	bladder
How do endoscopic bladder tumor resection techniques affect pathology practice? EAU Section of Uro-Technology (ESUT) and Uropathology (ESUP) survey.	PURPOSE: We aimed to examine how different endoscopic bladder tumor resection techniques affect pathologists' clinical practice patterns. METHODS: An online survey including 28 questions clustered in four main sections was prepared by the ESUT ERBT Working Group and released to the pathologists working in the institutions of experts of the ESUT Board and the working groups and experts in the uropathology working group. A descriptive analysis was performed using the collected data. RESULTS: Sixty-eight pathologists from 23 countries responded to the survey. 37.3% of the participants stated that they always report the T1 sub-staging. Of those who gave sub-staging, 61.3% used T1a, b. 85.2% think that en bloc samples provide spatial orientation faster than piecemeal samples, and 60% think en bloc samples are timesaving during an inspection. 55.7% stated that whether the tissue sample is en bloc or piecemeal is essential. 57.4% think en bloc sample reduces turnaround time and is cost-effective for 44.1%. A large number of pathologists find that the pathology examination of piecemeal samples has a longer learning curve. CONCLUSION: The survey shows that pathologists think that they can diagnose faster, accurately, and cost-effectively with ERBT samples, but they do not often encounter them in practice. Moreover, en bloc samples may be a better choice in pathology resident training. Evidence from real-life observational pathology practice and clinical research can reveal the current situation more clearly and increase awareness on proper treatment in endoscopic management of bladder tumors.	bladder
Enhancement of Farnesoid X Receptor Inhibits Migration, Adhesion and Angiogenesis through Proteasome Degradation and VEGF Reduction in Bladder Cancers.	(1) Background: Bladder cancer is a malignant tumor mainly caused by exposure to environmental chemicals, with a high recurrence rate. NR1H4, also known as Farnesoid X Receptor (FXR), acts as a nuclear receptor that can be activated by binding with bile acids, and FXR is highly correlated with the progression of cancers. The aim of this study was to verify the role of FXR in bladder cancer cells. (2) Methods: A FXR overexpressed system was established to investigate the effect of cell viability, migration, adhesion, and angiogenesis in low-grade TSGH8301 and high-grade T24 cells. (3) Results: After FXR overexpression, the ability of migration, adhesion, invasion and angiogenesis of bladder cancer cells declined significantly. Focal adhesive complex, MMP2, MMP9, and angiogenic-related proteins were decreased, while FXR was overexpressed in bladder cancer cells. Moreover, FXR overexpression reduced vascular endothelial growth factor mRNA and protein expression and secretion in bladder cancer cells. After treatment with the proteosome inhibitor MG132, the migration, adhesion and angiogenesis caused by FXR overexpression were all reversed in bladder cancer cells. (4) Conclusions: These results may provide evidence on the role of FXR in bladder cancer, and thus may improve the therapeutic efficacy of urothelial carcinoma in the future.	bladder